TY  - JOUR
AU  - Zorc, Minja
AU  - Škorput, Dubravko
AU  - Gvozdanović, Kristina
AU  - Margeta, Polona
AU  - Karolyi, Danijel
AU  - Luković, Zoran
AU  - Salajpal, Krešimir
AU  - Savić, Radomir
AU  - Munoz, Maria
AU  - Bovo, Samuele
AU  - Đurkin Kušec, Ivona
AU  - Radović, Čedomir
AU  - Kušec, Goran
AU  - Čandek Potokar, Marjeta
AU  - Dovč, Peter
PY  - 2022
UR  - http://r.istocar.bg.ac.rs/handle/123456789/818
AB  - Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established.
Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local
pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from
Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka
and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide
polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were
compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and
identifed genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).
Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka
and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed.
The analysis of admixture between breeds revealed potential gene fow between the Mangalitsa and Moravka, and
between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and
Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identifed
genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which
harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS
approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance.
Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the
existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to
estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed
genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under
selection pressure.
PB  - BMC
T2  - Genetic Selection Evolution
T1  - Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia
DO  - https://doi.org/10.1186/s12711-022-00718-6
ER  - 

@article{
author = "Zorc, Minja and Škorput, Dubravko and Gvozdanović, Kristina and Margeta, Polona and Karolyi, Danijel and Luković, Zoran and Salajpal, Krešimir and Savić, Radomir and Munoz, Maria and Bovo, Samuele and Đurkin Kušec, Ivona and Radović, Čedomir and Kušec, Goran and Čandek Potokar, Marjeta and Dovč, Peter",
year = "2022",
abstract = "Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established.
Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local
pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from
Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka
and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide
polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were
compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and
identifed genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).
Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka
and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed.
The analysis of admixture between breeds revealed potential gene fow between the Mangalitsa and Moravka, and
between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and
Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identifed
genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which
harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS
approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance.
Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the
existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to
estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed
genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under
selection pressure.",
publisher = "BMC",
journal = "Genetic Selection Evolution",
title = "Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia",
doi = "https://doi.org/10.1186/s12711-022-00718-6"
}

Zorc, M., Škorput, D., Gvozdanović, K., Margeta, P., Karolyi, D., Luković, Z., Salajpal, K., Savić, R., Munoz, M., Bovo, S., Đurkin Kušec, I., Radović, Č., Kušec, G., Čandek Potokar, M.,& Dovč, P.. (2022). Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. in Genetic Selection Evolution
BMC..
https://doi.org/https://doi.org/10.1186/s12711-022-00718-6

Zorc M, Škorput D, Gvozdanović K, Margeta P, Karolyi D, Luković Z, Salajpal K, Savić R, Munoz M, Bovo S, Đurkin Kušec I, Radović Č, Kušec G, Čandek Potokar M, Dovč P. Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. in Genetic Selection Evolution. 2022;.
doi:https://doi.org/10.1186/s12711-022-00718-6 .

Zorc, Minja, Škorput, Dubravko, Gvozdanović, Kristina, Margeta, Polona, Karolyi, Danijel, Luković, Zoran, Salajpal, Krešimir, Savić, Radomir, Munoz, Maria, Bovo, Samuele, Đurkin Kušec, Ivona, Radović, Čedomir, Kušec, Goran, Čandek Potokar, Marjeta, Dovč, Peter, "Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia" in Genetic Selection Evolution (2022),
https://doi.org/https://doi.org/10.1186/s12711-022-00718-6 . .